Open Microscopy Environment

Dear devs,

some days ago I tried to install the latest OMERO plugin for FiJi, but unfortunately the plugin complains about the missing "loci_tools.jar", alas, dropping that file into the "plugins" folder is nagging me with the attached error message on the next FiJi startup (though the OMERO plugin works fine then!).

FiJi is up to date, of course.

Any hints?
~Niko

Hi Nico,

Fiji is currently using the individual jars from Bio-Formats (from Maven) as opposed to the combined tools jar, which explains the duplication that you're seeing. Curtis recently updated the version of Bio-Formats that Fiji is pointing at. Could you try deleting the tools jar and running the Fiji updater?

Cheers,
~Josh.

Hi Josh,

I already deleted the tools jar (since otherwise FiJi would complain with every start), an re-running the updater doesn't show any new files.

Is it because I have the LOCI update repository for FiJi (http://dev.loci.wisc.edu/fiji/) included in our FiJi here?

Thanks
~Niko

Hi Nico,

Unfortunately, the OMERO.imagej plugin currently does not work with Fiji out of the box, due to the way the JAR files are structured. As you observed, OMERO.imagej explicitly checks for loci_tools.jar, which does not exist in a Fiji installation (rather, it is split into many smaller JARs).

However, there is a workaround: you can create a 0-byte file called loci_tools.jar and place it in your Fiji plugins folder. Then the OMERO.imagej plugin will be happy (having detected a file called "loci_tools.jar") and should proceed to work for you.

But downloading the "real" loci_tools.jar and placing it in your installation, as you have seen, will cause nothing but trouble, so I suggest not doing that.

Ah, perfect! I should have thought of that myself, especially since I already discovered that the plugin works regardless of the error message

Thanks, guys!
~Niko